week_9_rmarkdown

This is an R Markdown document. I can type whatever I want.

this is bold this is italic ### this will make the font smaller ##this will make it slightly bigger

Cheatsheet to these things here: https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf

save this file
to view in however it would be. use “knit” button

HTML : online only or knit it to a PDF or word doc to send to your PI (word can be funky) PDF does require additional download to work

You can click “insert” button for R or python or other code chunks OR ctrl+alt+i (PC) cmd+option+i (MAC) - use codechunk just like you would other script

SETTINGS: tell it to just output i nthe consol not inlline

TO not print when we knit :: warning=faslse message=false, echo=FALSE (don’t show code)

or FUNCTION to do this “suppress” for a single library suppressPackageStartupMessages(library(tidyverse))

library(tidyverse)
glimpse(storms)

## Observations: 10,010
## Variables: 13
## $ name        <chr> "Amy", "Amy", "Amy", "Amy", "Amy", "Amy", "Amy", "...
## $ year        <dbl> 1975, 1975, 1975, 1975, 1975, 1975, 1975, 1975, 19...
## $ month       <dbl> 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7,...
## $ day         <int> 27, 27, 27, 27, 28, 28, 28, 28, 29, 29, 29, 29, 30...
## $ hour        <dbl> 0, 6, 12, 18, 0, 6, 12, 18, 0, 6, 12, 18, 0, 6, 12...
## $ lat         <dbl> 27.5, 28.5, 29.5, 30.5, 31.5, 32.4, 33.3, 34.0, 34...
## $ long        <dbl> -79.0, -79.0, -79.0, -79.0, -78.8, -78.7, -78.0, -...
## $ status      <chr> "tropical depression", "tropical depression", "tro...
## $ category    <ord> -1, -1, -1, -1, -1, -1, -1, -1, 0, 0, 0, 0, 0, 0, ...
## $ wind        <int> 25, 25, 25, 25, 25, 25, 25, 30, 35, 40, 45, 50, 50...
## $ pressure    <int> 1013, 1013, 1013, 1013, 1012, 1012, 1011, 1006, 10...
## $ ts_diameter <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA...
## $ hu_diameter <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA...

library(viridis)

#create plot with pressure and something on xy axis 

ggplot(data=storms)+
  geom_jitter(aes(x= as.factor(month), y = pressure, fill=wind), pch= 21, alpha= .05)+
  scale_fill_viridis_c()+
  theme_bw()+
  labs(title= "Hurricane Pressure v Month", subtitle = "with Max Wind Speed", x = "Month")

writing out equations in Rmarkdown:

some instances this requires packages like Latex

If you want to write an equation, you put a $ on either side of it.

$\sum_{i=y}^n X_i$

library(knitr)

kable(head(storms),caption="table using kable")

table using kable
name	year	month	day	hour	lat	long	status	category	wind	pressure	ts_diameter	hu_diameter
Amy	1975	6	27	0	27.5	-79.0	tropical depression	-1	25	1013	NA	NA
Amy	1975	6	27	6	28.5	-79.0	tropical depression	-1	25	1013	NA	NA
Amy	1975	6	27	12	29.5	-79.0	tropical depression	-1	25	1013	NA	NA
Amy	1975	6	27	18	30.5	-79.0	tropical depression	-1	25	1013	NA	NA
Amy	1975	6	28	0	31.5	-78.8	tropical depression	-1	25	1012	NA	NA
Amy	1975	6	28	6	32.4	-78.7	tropical depression	-1	25	1012	NA	NA

htmlTable::htmlTable(head(storms))

	name	year	month	day	hour	lat	long	status	category	wind	pressure
1	Amy	1975	6	27	0	27.5	-79	tropical depression	-1	25	1013
2	Amy	1975	6	27	6	28.5	-79	tropical depression	-1	25	1013
3	Amy	1975	6	27	12	29.5	-79	tropical depression	-1	25	1013
4	Amy	1975	6	27	18	30.5	-79	tropical depression	-1	25	1013
5	Amy	1975	6	28	0	31.5	-78.8	tropical depression	-1	25	1012
6	Amy	1975	6	28	6	32.4	-78.7	tropical depression	-1	25	1012

#make an interactive table 
DT::datatable(storms)

## Warning in instance$preRenderHook(instance): It seems your data is too
## big for client-side DataTables. You may consider server-side processing:
## https://rstudio.github.io/DT/server.html

library(plotly)

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

ggplotly(
  ggplot(data=storms)+
  geom_jitter(aes(x= as.factor(month), y = pressure, fill=wind), pch= 21, alpha= .05)+
  scale_fill_viridis_c()+
  theme_bw()+
  labs(title= "Hurricane Pressure v Month", subtitle = "with Max Wind Speed", x = "Month"))

## Warning in L$marker$color[idx] <- aes2plotly(data, params, "fill")[idx]:
## number of items to replace is not a multiple of replacement length

R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

summary(cars)

##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

Including Plots

You can also embed plots, for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

week_9_rmarkdown

Christine Parisek

3/5/2019

R Markdown

Including Plots